Re: HDF5 error with gmt 4.5.12
Joaquim Luis <[email protected]> Sat, 16 Aug 2014 12:18:15 +0100
| Newsgroups | gmane.comp.gis.gmt.user |
|---|---|
| Message-ID | <[email protected]> |
--Apple-Mail-6C11ADD8-695D-4815-99D4-278C2F349E0E Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Well, it wasn't me who said that GMT complained about a HDF version mismatch= , and GMT doesn't access HDF directly. Only via GDAL.=20 Sent from my iDedo No dia 16/08/2014, =C3=A0s 10:51, "Gery ." <[email protected]> escreveu:= > So, that HDF thing is only to use gdal?? great! because I don't link gdal w= ith GMT, so you are wrong Joaquim!! =3D) Cygwin sucks perhaps for you, for m= e it works well. Based on that, why it sucks? why are you guys so angry with= Cygwin? I think you just need to relief that feeling and be free! ;) >=20 > Cheers, and be happy! >=20 > Sent from my iRon >=20 > On Aug 16, 2014, at 1:40, "Joaquim Luis" <[email protected]> wrote: >=20 > Gery, >=20 > That warning from HDF essentially means that you are screwed. The computer= will blow, or at least you'll get a crash. The HDF version used to link GDA= L and the one at use must be exactly the same. > Still, on the land of opinions, Cygwin sucks compared with with MinGW wher= e you can just use the, way faster, GMT5 Win binaries provided by us.=20 >=20 > Sent from my iPadiola >=20 >> On 15/08/2014, at 12:57, "Gery ." <[email protected]> wrote: >>=20 >> Sorry for the last noisy message, but things were smooth finally, the sol= ution was to install without gdal. Now things work, but I received this mess= age about HDF5: >>=20 >> -----------------------------------------------------------=E2=80=8B >> $ pscoast -R-71.2/-70.9/42.25/42.45 -JM6.0 -Ba0.05f0.01SWen -Ia -Na -W3 -= K > ps >>=20 >> Warning! ***HDF5 library version mismatched error*** >>=20 >> The HDF5 header files used to compile this application do not match >>=20 >> the version used by the HDF5 library to which this application is linked.= >>=20 >> Data corruption or segmentation faults may occur if the application conti= nues. >>=20 >> This can happen when an application was compiled by one version of HDF5 b= ut >>=20 >> linked with a different version of static or shared HDF5 library. >>=20 >> You should recompile the application or check your shared library related= >>=20 >> settings such as 'LD_LIBRARY_PATH'. >>=20 >> You can, at your own risk, disable this warning by setting the environmen= t >>=20 >> variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'. >>=20 >> Setting it to 2 or higher will suppress the warning messages totally. >>=20 >> Headers are 1.8.12, library is 1.8.13 >>=20 >> SUMMARY OF THE HDF5 CONFIGURATION >>=20 >> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D >>=20 >> General Information: >>=20 >> ------------------- >>=20 >> HDF5 Version: 1.8.13 >>=20 >> Configured on: Wed Jun 4 15:04:57 CEST 2014 >>=20 >> Configured by: marco@GE-MATZERI-EU >>=20 >> Configure mode: production >>=20 >> Host system: i686-pc-cygwin >>=20 >> Uname information: CYGWIN_NT-6.1-WOW64 GE-MATZERI-EU 1.7.30(0.272/5/3) 20= 14-05-23 10:36 i686 Cygwin >>=20 >> Byte sex: little-endian >>=20 >> Libraries: shared >>=20 >> Installation point: /usr >>=20 >> Compiling Options: >>=20 >> ------------------ >>=20 >> Compilation Mode: production >>=20 >> C Compiler: /usr/bin/gcc >>=20 >> CFLAGS: -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-ma= p=3D/pub/devel/hdf5/hdf5-1.8.13-1/ build=3D/usr/src/debug/= hdf5-1.8.13-1 -fdebug-prefix-map=3D/pub/devel/hdf5/hdf5-1.8.13-1/src/hdf5-1.= 8.13=3D/usr/src/debug/hdf5-1.8.13-1 >>=20 >> H5_CFLAGS: -std=3Dc99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-= arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconvers= ion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-de= clarations -Wre dundant-decls -Wnested-externs -Winline -Wfloat-equal -Wmiss= ing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimizati on -W= format=3D2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -= Wold-style-definition -Winvalid-pch -Wvariadic-macr os -Winit-self -Wmissing= -include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-o= ptimizations -Wc++-compat -Wst rict-overflow -Wlogical-op -Wlarger-than=3D20= 48 -Wvla -Wsync-nand -Wframe-larger-than=3D16384 -Wpacked-bitfield-compat -W= strict-overfl ow=3D5 -Wjump-misses-init -Wunsuffixed-float-constants -Wdoubl= e-promotion -Wsuggest-attribute=3Dconst -Wtrampolines -Wstack-usage=3D8192 -= Wvector-operation-performance -Wsuggest-attribute=3Dpure -Wsuggest-attribute= =3Dnoreturn -Wsuggest-attribute=3Dformat -O3 -fomit-frame- pointer -finline-= functions >>=20 >> AM_CFLAGS: >>=20 >> CPPFLAGS: >>=20 >> H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API >>=20 >> AM_CPPFLAGS: >>=20 >> Shared C Library: yes >>=20 >> Static C Library: no >>=20 >> Statically Linked Executables: no >>=20 >> LDFLAGS: >>=20 >> H5_LDFLAGS: -no-undefined >>=20 >> AM_LDFLAGS: >>=20 >> Extra libraries: -lz -ldl -lm >>=20 >> Archiver: ar >>=20 >> Ranlib: ranlib >>=20 >> Debugged Packages: >>=20 >> API Tracing: no >>=20 >> Languages: >>=20 >> ---------- >>=20 >> Fortran: no >>=20 >> C++: yes >>=20 >> C++ Compiler: /usr/bin/g++ >>=20 >> C++ Flags: -ggdb -O2 -pipe -fdebug-prefix-map=3D/pub/devel/hdf5/hdf5-1.8.= 13-1/build=3D/usr/src/debug/hdf5-1.8.13 -1 -fdebug-prefix-map=3D/pub/devel/h= df5/hdf5-1.8.13-1/src/hdf5-1.8.13=3D/usr/src/debug/hdf5-1.8.13-1 >>=20 >> H5 C++ Flags: >>=20 >> AM C++ Flags: >>=20 >> Shared C++ Library: yes >>=20 >> Static C++ Library: no >>=20 >> Features: >>=20 >> --------- >>=20 >> Parallel HDF5: no >>=20 >> High Level library: yes >>=20 >> Threadsafety: no >>=20 >> Default API Mapping: v18 >>=20 >> With Deprecated Public Symbols: yes >>=20 >> I/O filters (external): deflate(zlib) >>=20 >> I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset >>=20 >> MPE: no >>=20 >> Direct VFD: yes >>=20 >> dmalloc: no >>=20 >> Clear file buffers before write: yes >>=20 >> Using memory checker: no >>=20 >> Function Stack Tracing: no >>=20 >> Strict File Format Checks: no >>=20 >> Optimization Instrumentation: no >>=20 >> Large File Support (LFS): yes >>=20 >> Bye... >>=20 >> Aborted (core dumped) >>=20 >> ----------------------------------------------------------- >>=20 >> I have the latest Cygwin 32-bit version. Which HDF5 version should I use?= this Cygwin comes with hdf5 1.8.13-1, netcdf 4.3.2-1 and zlib 1.2.8-1. >>=20 >> Any ideas?? thank.. >>=20 >> Gery >>=20 >> Mailing list for GMT discussions of all kinds. If you are not sure you ha= ve found a bug, discuss it here first. To formally report bugs or request fe= atures, please register and add New Issue on gmt.soest.hawaii.edu To unsubsc= ribe, send the message "signoff gmt-help" to [email protected] Note:= gmt-help will become obsolete on Sept 1, 2014 - please use forum on gmt.soe= st.hawaii.edu instead. > Mailing list for GMT discussions of all kinds. If you are not sure you hav= e found a bug, discuss it here first. To formally report bugs or request fea= tures, please register and add New Issue on gmt.soest.hawaii.edu To unsubscr= ibe, send the message "signoff gmt-help" to [email protected] Note: g= mt-help will become obsolete on Sept 1, 2014 - please use forum on gmt.soest= .hawaii.edu instead. > Mailing list for GMT discussions of all kinds. If you are not sure you hav= e found a bug, discuss it here first. To formally report bugs or request fea= tures, please register and add New Issue on gmt.soest.hawaii.edu To unsubscr= ibe, send the message "signoff gmt-help" to [email protected] Note: g= mt-help will become obsolete on Sept 1, 2014 - please use forum on gmt.soest= .hawaii.edu instead. Mailing list for GMT discussions of all kinds. If you are not sure you have found a bug, discuss it here first. To formally report bugs or request features, please register and add New Issue on gmt.soest.hawaii.edu To unsubscribe, send the message "signoff gmt-help" to [email protected] Note: gmt-help will become obsolete on Sept 1, 2014 - please use forum on gmt.soest.hawaii.edu instead. --Apple-Mail-6C11ADD8-695D-4815-99D4-278C2F349E0E Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable <html><head><meta http-equiv=3D"content-type" content=3D"text/html; charset=3D= utf-8"></head><body dir=3D"auto"><div>Well, it wasn't me who said that GMT c= omplained about a HDF version mismatch, and GMT doesn't access HDF directly.= Only via GDAL. <br><br><div>Sent from my iDedo</div></div><div><br>No d= ia 16/08/2014, =C3=A0s 10:51, "Gery ." <<a href=3D"mailto:gamejihou@HOTMA= IL.COM">[email protected]</a>> escreveu:<br><br></div><blockquote typ= e=3D"cite"><div><meta http-equiv=3D"content-type" content=3D"text/html; char= set=3Dutf-8"><div>So, that HDF thing is only to use gdal?? great! because I d= on't link gdal with GMT, so you are wrong Joaquim!! =3D) Cygwin sucks perhap= s for you, for me it works well. Based on that, why it sucks? why are you gu= ys so angry with Cygwin? I think you just need to relief that feeling and be= free! ;)</div><div><br></div><div>Cheers, and be happy!<br><br>Sent from my= iRon</div><div><br>On Aug 16, 2014, at 1:40, "Joaquim Luis" <<a href=3D"= mailto:[email protected]">[email protected]</a>> wrote:<br><br></div><div= ><meta http-equiv=3D"content-type" content=3D"text/html; charset=3Dutf-8"><d= iv>Gery,</div><div><br></div><div>That warning from HDF essentially means th= at you are screwed. The computer will blow, or at least you'll get a crash. T= he HDF version used to link GDAL and the one at use must be exactly the same= .</div><div>Still, on the land of opinions, Cygwin sucks compared with with M= inGW where you can just use the, way faster, GMT5 Win binaries provided by u= s. <br><br>Sent from my iPadiola</div><div><br>On 15/08/2014, at 12:57,= "Gery ." <<a href=3D"mailto:[email protected]">[email protected]= </a>> wrote:<br><br></div><blockquote type=3D"cite"><div> <meta name=3D"generator" content=3D"Windows Mail 17.5.9600.20573"> <style data-externalstyle=3D"true"><!-- p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph { margin-top:0in; margin-right:0in; margin-bottom:0in; margin-left:.5in; margin-bottom:.0001pt; } p.MsoNormal, li.MsoNormal, div.MsoNormal { margin:0in; margin-bottom:.0001pt; } p.MsoListParagraphCxSpFirst, li.MsoListParagraphCxSpFirst, div.MsoListParagr= aphCxSpFirst,=20 p.MsoListParagraphCxSpMiddle, li.MsoListParagraphCxSpMiddle, div.MsoListPara= graphCxSpMiddle,=20 p.MsoListParagraphCxSpLast, li.MsoListParagraphCxSpLast, div.MsoListParagrap= hCxSpLast { margin-top:0in; margin-right:0in; margin-bottom:0in; margin-left:.5in; margin-bottom:.0001pt; line-height:115%; } --></style> <div data-externalstyle=3D"false" dir=3D"ltr" style=3D"font-family: 'Calibri= ', 'Segoe UI', 'Meiryo', 'Microsoft YaHei UI', 'Microsoft JhengHei UI', 'Mal= gun Gothic', 'sans-serif';font-size:12pt;"><div>Sorry for the last noisy mes= sage, but things were smooth finally, the solution was to install without gd= al. Now things work, but I received this message about HDF5:</div><div><br><= /div><div>-----------------------------------------------------------=E2=80=8B= </div><div><p>$ pscoast -R-71.2/-70.9/42.25/42.45 -JM6.0 -Ba0.05f0.01SWen -I= a -Na -W3 -K > ps</p><p>Warning! ***HDF5 library version mismatched error= ***</p></div><div> <p>The HDF5 header files used to compile this application do not match</p> <p>the version used by the HDF5 library to which this application is linked.= </p> <p>Data corruption or segmentation faults may occur if the application conti= nues.</p> <p>This can happen when an application was compiled by one version of HDF5 b= ut</p> <p>linked with a different version of static or shared HDF5 library.</p> <p>You should recompile the application or check your shared library related= </p> <p>settings such as 'LD_LIBRARY_PATH'.</p> <p>You can, at your own risk, disable this warning by setting the environmen= t</p> <p>variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.</p> <p>Setting it to 2 or higher will suppress the warning messages totally.</p>= <p>Headers are 1.8.12, library is 1.8.13</p> <p> SUMMARY OF THE HDF5 CONFIGURATION</p> <p> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D</p> <p>General Information:</p> <p>-------------------</p> <p> HDF5 Version: 1.8.13</p> <p> Configured on: Wed Jun 4 15:04:57 CEST 2014</p> <p> Configured by: marco@GE-MATZERI-EU</p> <p> Configure mode: production</p> <p> Host system: i686-pc-cygwin</p> <p> Uname information: CYGWIN_NT-6.1-WOW64 GE-MATZERI-EU 1.7.30= (0.272/5/3) 2014-05-23 10:36 i686 Cygwin</p> <p> Byte sex: little-endian</p> <p> Libraries: shared</p> <p> Installation point: /usr</p> <p>Compiling Options:</p> <p>------------------</p> <p> Compilation Mode: production</p> <p> C Compiler: /usr/bin/gcc</p> <p> CFLAGS: -ggdb -O2 -pipe -Wimplicit-function-decl= aration -fdebug-prefix-map=3D/pub/devel/hdf5/hdf5-1.8.13-1/ = build=3D/usr/src/debug/hdf5-1.8.13-1 -fdebug-prefix-map=3D/pub/devel/hdf5/= hdf5-1.8.13-1/src/hdf5-1.8.13=3D/usr/src/debug/hdf5-1.8.13-1</p> <p> H5_CFLAGS: -std=3Dc99 -pedantic -Wall -Wextra -Wund= ef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual = -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-pro= totypes -Wmissing-prototypes -Wmissing-declarations -Wre d= undant-decls -Wnested-externs -Winline -Wfloat-equal -Wmissing-format-attrib= ute -Wmissing-noreturn -Wpacked -Wdisabled-optimizati on -= Wformat=3D2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -= Wold-style-definition -Winvalid-pch -Wvariadic-macr os -Wi= nit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macr= os -Wunsafe-loop-optimizations -Wc++-compat -Wst rict-over= flow -Wlogical-op -Wlarger-than=3D2048 -Wvla -Wsync-nand -Wframe-larger-than= =3D16384 -Wpacked-bitfield-compat -Wstrict-overfl ow=3D5 -= Wjump-misses-init -Wunsuffixed-float-constants -Wdouble-promotion -Wsuggest-= attribute=3Dconst -Wtrampolines -Wstack-usage=3D8192 -Wve= ctor-operation-performance -Wsuggest-attribute=3Dpure -Wsuggest-attribute=3D= noreturn -Wsuggest-attribute=3Dformat -O3 -fomit-frame- po= inter -finline-functions</p> <p> AM_CFLAGS:</p> <p> CPPFLAGS:</p> <p> H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API</p> <p> AM_CPPFLAGS:</p> <p> Shared C Library: yes</p> <p> Static C Library: no</p> <p> Statically Linked Executables: no</p> <p> LDFLAGS:</p> <p> H5_LDFLAGS: -no-undefined</p> <p> AM_LDFLAGS:</p> <p> Extra libraries: -lz -ldl -lm</p> <p> Archiver: ar</p> <p> Ranlib: ranlib</p> <p> Debugged Packages:</p> <p> API Tracing: no</p> <p>Languages:</p> <p>----------</p> <p> Fortran: no</p> <p> C++: yes</p> <p> C++ Compiler: /usr/bin/g++</p> <p> C++ Flags: -ggdb -O2 -pipe -fdebug-prefix-map=3D/pu= b/devel/hdf5/hdf5-1.8.13-1/build=3D/usr/src/debug/hdf5-1.8.13 = -1 -fdebug-prefix-map=3D/pub/devel/hdf5/hdf5-1.8.13-1/src/hdf5-1.8.13=3D= /usr/src/debug/hdf5-1.8.13-1</p> <p> H5 C++ Flags:</p> <p> AM C++ Flags:</p> <p> Shared C++ Library: yes</p> <p> Static C++ Library: no</p> <p>Features:</p> <p>---------</p> <p> Parallel HDF5: no</p> <p> High Level library: yes</p> <p> Threadsafety: no</p> <p> Default API Mapping: v18</p> <p> With Deprecated Public Symbols: yes</p> <p> I/O filters (external): deflate(zlib)</p> <p> I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset</p> <p> MPE: no</p> <p> Direct VFD: yes</p> <p> dmalloc: no</p> <p>Clear file buffers before write: yes</p> <p> Using memory checker: no</p> <p> Function Stack Tracing: no</p> <p> Strict File Format Checks: no</p> <p> Optimization Instrumentation: no</p> <p> Large File Support (LFS): yes</p> <p>Bye...</p> <p>Aborted (core dumped)</p><p>---------------------------------------------= --------------</p></div><div>I have the latest Cygwin 32-bit version. Which H= DF5 version should I use? this Cygwin comes with hdf5 1.8.13-1, netcdf 4.3.2= -1 and zlib 1.2.8-1.</div><div>= <br></div><div>Any ideas?? thank..</div><div><br></div><div>Gery</div><div><= br></div> </div> Mailing list for GMT discussions of all kinds. If you are not sure you have= found a bug, discuss it here first. To formally report bugs or request features, please register and add New Iss= ue on <a href=3D"http://gmt.soest.hawaii.edu">gmt.soest.hawaii.edu</a> To unsubscribe, send the message "signoff gmt-help" to <a href=3D"mailto:lis= [email protected]">[email protected]</a> Note: gmt-help will become obsolete on Sept 1, 2014 - please use forum on <a= href=3D"http://gmt.soest.hawaii.edu">gmt.soest.hawaii.edu</a> instead. </div></blockquote>Mailing list for GMT discussions of all kinds. If you ar= e not sure you have found a bug, discuss it here first. To formally report bugs or request features, please register and add New Iss= ue on <a href=3D"http://gmt.soest.hawaii.edu">gmt.soest.hawaii.edu</a> To unsubscribe, send the message "signoff gmt-help" to <a href=3D"mailto:lis= [email protected]">[email protected]</a> Note: gmt-help will become obsolete on Sept 1, 2014 - please use forum on <a= href=3D"http://gmt.soest.hawaii.edu">gmt.soest.hawaii.edu</a> instead. </div> Mailing list for GMT discussions of all kinds. If you are not sure you have= found a bug, discuss it here first. To formally report bugs or request features, please register and add New Iss= ue on <a href=3D"http://gmt.soest.hawaii.edu">gmt.soest.hawaii.edu</a> To unsubscribe, send the message "signoff gmt-help" to <a href=3D"mailto:lis= [email protected]">[email protected]</a> Note: gmt-help will become obsolete on Sept 1, 2014 - please use forum on <a= href=3D"http://gmt.soest.hawaii.edu">gmt.soest.hawaii.edu</a> instead. </div></blockquote></body></html>= Mailing list for GMT discussions of all kinds. If you are not sure you have found a bug, discuss it here first. To formally report bugs or request features, please register and add New Issue on gmt.soest.hawaii.edu To unsubscribe, send the message "signoff gmt-help" to <a href=3D"mailto:[email protected]">[email protected]</a> Note: gmt-help will become obsolete on Sept 1, 2014 - please use forum on gmt.soest.hawaii.edu instead. --Apple-Mail-6C11ADD8-695D-4815-99D4-278C2F349E0E--